Enhancing Structure Prediction and Design of Soluble and Membrane Proteins with Explicit Solvent-Protein Interactions

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Recently, single-particle cryo-electron microscopy emerged as a technique capable of determining protein structures at near-atomic resolution and resolving protein dynamics with a temporal resolution ranging from second to milliseconds. This thesis describ ...

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Microsecond time-resolved cryo-electron microscopy

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Microsecond time-resolved cryo-electron microscopy has emerged as a novel approach for directly observing protein dynamics. By providing microsecond temporal and near-atomic spatial resolution, it has the potential to elucidate a wide range of dynamics tha ...

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Accessing the thermal transport properties of glasses is a major issue for the design of production strategies of glass industry, as well as for the plethora of applications and devices where glasses are employed. From the computational standpoint, the che ...

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Over the past two decades, protein S-acylation (often referred to as S-palmitoylation) has emerged as an important regulator of vital signalling pathways. S-Acylation is a reversible post-translational modification that involves the attachment of a fatty a ...

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Efficient and insightful descriptors for representing molecular and material space

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Data-driven approaches have been applied to reduce the cost of accurate computational studies on materials, by using only a small number of expensive reference electronic structure calculations for a representative subset of the materials space, and using ...

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Recording physiological history of cells with chemical labeling

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Recordings of the physiological history of cells provide insights into biological processes, yet obtaining such recordings is a challenge. To address this, we introduce a method to record transient cellular events for later analysis. We designed proteins t ...

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Membrane specificity of the human cholesterol transfer protein STARD4

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STARD4 regulates cholesterol homeostasis by transferring cholesterol between the plasma membrane and endoplasmic reticulum. The STARD4 structure features a helix-grip fold surrounding a large hydrophobic cavity holding the sterol. Its access is controlled ...

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One of the goals of synthetic biology is the development of an artificial cell. Building an artificial cell from scratch will provide a deeper understanding of fundamental mechanisms and models in biology and promises to contribute towards building novel p ...

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Peptide-based virucidal drugs

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Before the COVID-19 pandemic, viruses were not a major priority for the scientific community. Today, many events have changed the world and the importance of studying viruses, vaccines, and antiviral drugs is fully appreciated. The development of effective ...

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Oxidative Defect Detection Within Free and Packed DNA Systems: A Quantum Mechanical/Molecular Mechanics (QM/ MM) Approach

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Base excision repair enzymes (BERs) detect and repair oxidative DNA damage with efficacy despite the small size of the defects and their often only minor structural impact. A charge transfer (CT) model for rapid scanning of DNA stretches has been evoked to ...

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A new self-adjustable glaucoma valve

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Introduction: Glaucoma, the leading cause of irreversible blindness globally, affects more than 70 million people across the world. When initial treatments prove ineffective, especially for cases with high intraocular pressure (IOP), the preferred approach ...

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Quantified interface chemistry and biophysics via water imaging

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High throughput wide-field second harmonic imaging enables the label-free imaging of interfacial (< 3 nm thick) water, with a spatial resolution of similar to 370 nm using similar to 100 ms acquisition times per image. The obtained interfacial orientationa ...

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